Found out decision. In order to hide zero values you should create js script in your xhtml file and then bind this script to model with org.primefaces.model.chart.BarChartModel.setExtender method.
<script>
function extender() {
this.cfg.seriesDefaults = {
showMarker: true,
renderer: $.jqplot.BarRenderer,
pointLabels: {show: true, location: 'n', ypadding: 0, hideZeros: true}
};
}
</script>
Java Class:
BarChartModel model = new BarChartModel();
model.setShowDatatip(false);
model.setShowPointLabels(true);
model.setExtener("extender");
xhtml
<p:chart type="bar" model="#{'javaClassController.getModel()'}"/>
Result should look like this: